How to untwist a twisted STL model from microCT scanning
Solved! Turns out the Simple Deform modifier works perfectly for this type of thing! 

Steps for Blender 2.81:


Import the STL file into Blender using File, Import, Stl
If required, rotate the model so that the twist axis is aligned with the X, Y or Z axis
In Object mode, select the entire STL object
Go to the Modifier tab and select the Simple Deform modifier. By default the Twist operation will be selected.
Select the axis along which the twist in the model is aligned.
Adjust the Deform Angle until the twist is removed or at least as small as you can get it.
To save the corrected STL, go to File, Export, Stl, give it a different filename and click Export STL.